The influence of transcript assembly on the proteogenomics discovery of microproteins
Fig 3
MAPS and Cufflinks find complementary micropreteins.
A) Proposed microprotein discovery workflow incorporating Cufflinks and MAPS assemblies to improve microprotein discovery B) Total number of unique curated microproteins detected by mass spectrometry in HEK293T cells. Cell lysate was enriched using ACID or C8-SPE Column (data combined), and proteomics data was searched against Cufflinks or MAPS assembled transcriptome that was translated in three frames. C) Distribution of microproteins uniquely detected in Cufflinks database search (eight microproteins, left) and MAPS database search (23 microproteins, right), describing reasons why they were not detected in the alternate. Alt. Threshold: microprotein-containing transcript was filtered from one assembly while kept in the other due to differences in abundance thresholds, Alt. splicing: microprotein was translated from a transcript with alternate splicing event, Proteomics search: microproteins were not detected due to similar sequence present during MS search, Alt. exon usage: microproteins arise from extension of exons, Anti-sense: transcript on only one strand is assembled.